Background. Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organisms environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity.. Results. The regression analyses indicated that GCVAR was significantly associated with domain (i.e. archaea or bacteria), phylum, and oxygen requirement. GCVAR was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found ...
The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes. The most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the variation correlates with CpG frequencies in vertebrates but not in invertebrates and it also correlates with gene expression, especially in mammals. We also detect GC and AT skews in all clades (where %G is not equal to %C or %A is not equal to %T respectively) but these occur
Your gene comprises long repeats, secondary structures or a really high or low GC content? With our specified protocol for complex genes we are able to synthesise also the intricates.
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Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Meloidogyne graminicola.Numbers on the Y-axis refer to the total number of codons (A)
Polyomaviruses (PyVs) have a wide range of hosts, from humans to fish, and their effects on hosts vary. The differences in the infection characteristics of PyV with respect to the host are assumed to be influenced by the biochemical function of the LT-Ag protein, which is related to the cytopathic effect and tumorigenesis mechanism via interaction with the host protein. We carried out a comparative analysis of codon usage patterns of large T-antigens (LT-Ags) of PyVs isolated from various host species and their functional domains and sequence motifs. Parity rule 2 (PR2) and neutrality analysis were applied to evaluate the effects of mutation and selection pressure on codon usage bias. To investigate evolutionary relationships among PyVs, we carried out a phylogenetic analysis, and a correspondence analysis of relative synonymous codon usage (RSCU) values was performed. Nucleotide composition analysis using LT-Ag gene sequences showed that the GC and GC3 values of avian PyVs were higher than those of
BACKGROUND:The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.RESULTS:Here we compare expression data from Pinus taeda cDNA microarrays using transcripts amplified either exponentially by PCR or linearly by T7 transcription. The amplified transcripts vary significantly in estimated length, GC content and expression depending on amplification technique. Amplification by T7 RNA polymerase gives transcripts with a greater range of lengths, greater estimated mean length, and greater variation of expression levels, but lower average GC content, than those from PCR amplification. For genes with significantly higher expression after T7 transcription than after PCR, the transcripts were 27% longer and had about 2 percentage units lower GC content. The correlation of expression intensities between ...
TY - JOUR. T1 - Protein elemental sparing and codon usage bias are correlated among bacteria. AU - Bragg, Jason G.. AU - Quigg, Antonietta. AU - Raven, John A.. AU - Wagner, Andreas. PY - 2012/5. Y1 - 2012/5. N2 - Highly expressed proteins can exhibit relatively small material costs, in terms of the quantities of carbon (C), nitrogen (N) or sulphur (S) atoms they contain. This elemental sparing probably reflects selection to reduce the quantities of potentially growth-limiting elements in abundant proteins, but the evolutionary mechanisms for adaptive elemental sparing are still poorly understood. Here, we predict that the extent of elemental sparing in highly expressed proteins will vary among organisms, according to the effectiveness of selection in determining the fate of mutations. We test this hypothesis in bacteria by asking whether elemental sparing is correlated with codon usage bias. Bacteria exhibit extraordinary variation in their life histories and demography and consequently in the ...
Results for QLV parameters A, B, and τ2, and typical stress relaxation curve fits for IM and EX. A was significantly decreased in injured groups relative to CTL. A was significantly increased in the IM group compared to the EX and CA groups. B was significantly decreased in injured groups relative to CTL. B was significantly increased in the IM group compared to the EX and CA groups. τ2 was significantly decreased in the CA and EX groups relative to CTL. τ2 was significantly increased in the IM group compared to the EX groups. The IM group had a higher peak stress, and maintained this stress for a longer period of time, than the EX group. (Mean +/− standard deviation, *: significant difference relative to CTL [p,0.05], # significant difference due to activity level [p,0.05 ...
General Information: Environment: Soil; Isolation: Coal-cleaning residues; Temp: Mesophile; Temp: 30C. This genus comprises about 150 metabolically diverse species of anaerobes that are ubiquitous in virtually all anoxic habitats where organic compounds are present, including soils, aquatic sediments and the intestinal tracts of animals and humans. This shape is attributed to the presence of endospores that develop under conditions unfavorable for vegetative growth and distend single cells terminally or sub-terminally. Spores germinate under conditions favorable for vegetative growth, such as anaerobiosis and presence of organic substrates. It is believed that present day Mollicutes (Eubacteria) have evolved regressively (i.e., by genome reduction) from gram-positive clostridia-like ancestors with a low GC content in DNA. Known opportunistic toxin-producing pathogens in animals and humans. Some species are capable of producing organic solvents (acetone, ethanol, etc,), molecular hydrogen and ...
Because of polymer complexity, property variability must be taken into consideration. In this section, we will discuss possible sources of polymer inconsistency and offer suggestions to recognize and reduce these errors. Chemical or compositional heterogeneity refers to the chemical or structural difference among chains of the same polymer. Thus a measured property of a chemically heterogeneous sample will be an averaged value dependent upon sample source. For chemically homogeneous samples, property variability will not be a concern. In a similar fashion, polymers that are polydisperse in molecular weight have averaged property values, while monodisperse samples will give accurate data. Obviously, samples that are both chemically homogeneous and monodisperse will give the most accurate and precise values. As compared to synthetic polymers, almost all nucleic acids and mammalian proteins are compositionally (chemically) homogeneous and monodisperse, if not there would be no life; biopolymers ...
Application of chemical engineering principles to the study of tumor formation and treatment is fertile new ground for research and is necessary for the advancement of cancer therapy. Over the last century, researchers have discovered many of the genetic causes of cancer and yet nearly 46,000 people will die this year from cancer in the United States alone. Standard cancer therapies often fail because of spatial heterogeneity of nutrients, wastes, and therapeutics. Transport barriers prevent therapeutic agents from reaching effective concentrations throughout tumors. Models based on mass balance, transport phenomena and reaction kinetics are powerful tools able clarify the connection between the genetic aberrations and the compositional heterogeneity of tumors. Therapeutic strategies designed using engineering principles will be able to overcome transport barriers and create more effective therapies.. Single treatments of radiation or chemotherapy often do not kill all cancer cells within a ...
The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options ...
The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options ...
Empirical studies have shown that human beings cannot normally perceive changes in numeric data (e.g. price movements) occurring more frequently than once every 200ms.. Consequently for applications that have a human as their primary user, a useful rule of thumb is that Stop-The-World (STW) pause of 200ms or under is usually of no concern. Some applications (e.g. streaming video) need lower GC jitter than this, but many GUI applications will not. ...
DNA - A double helix DNA stands for Deoxyribonucleic acid.It is a nucleic which is used for storing information for long term in all living beings and some viruses. Base composition in DNA varies from one species to other but in all the cases the amount of adenine is equal to thymine and the amount
The species page of Empusa sp. IRT-2002. Also know as (German: große Mantiden). Information about genome files, completeness, GC-content, size, N50-values, and sequencing methods are listed.
The species page of Magnaporthe sp. MG12. . Information about genome files, completeness, GC-content, size, N50-values, and sequencing methods are listed.
德者,內也;得者,外也。「上德不德」,言其神不淫於外也。 神不淫於外則身全,身全之謂德。德者,得身也。凡德者,以無為集,以無欲成; 以不思安,以不用固。為之欲之,則德無舍;德無舍則不全。用之思之則不固,不固則無功, 無功則生於德。德則無德,不德則(在)有德。故曰:「上德不德,是以有德。」 所以貴無為無思為虛者,謂其意無所制也。夫無術者,故以無為無思為虛也。 夫故以無為無思為虛者,其意常不忘虛,是制於為虛也。虛者,謂其意(所無)〔無所〕制也。 今制於為虛,是不虛也。虛者之無為也,不以無為為有常。不以無為為有常,則虛;虛,則德盛; 德盛之謂上德。故曰:「上德無為而無不為也。」 仁者,謂其中心欣然愛人也;其喜人之有福,而惡人之有禍也;生心之所不能已也, ...
Strain 10-1-101T, isolated from a sand sample collected from the desert of Xinjiang, China, was a Gram-negative, aerobic, motile, rod-shaped bacterium. Colonies grown on 0.1× trypticase soy broth agar were circular, convex and light-pink-coloured. The major cellular fatty acids of the novel strain were C18 : 1 ω7c (72.71 %) and C16 : 0 (7.05 %). The DNA G+C content of strain 10-1-101T was 68.8 mol% and Q-10 was the major respiratory quinone. 16S rRNA gene sequence analysis indicated that strain 10-1-101T was related to type strains of the genus Skermanella, with sequence similarity values of 94.07 % with Skermanella aerolata DSM 18479T and 92.74 % with Skermanella parooensis DSM 9527T. On the basis of genotypic, phenotypic and phylogenetic data, this new strain represents a novel species of the genus Skermanella, for which the name Skermanella xinjiangensis sp. nov. is proposed. The type strain is 10-1-101T (=CCTCC AB 207153T=NRRL B-51273T).
A Gram-negative, rod-shaped, non-motile and pink bacterial strain, designated strain GCM0142T, was isolated from the confined seawater in the Saemangeum Tide Embankment of South Korea, and characterized using a polyphasic approach. 16S rRNA gene sequence analysis of strain GCM0142T indicated that the isolate belonged to the phylum Bacteroidetes and exhibited similarity levels of 94.0-96.4 % to the type strains of recognized Pontibacter species. Strain GCM0142T was oxidase- and catalase-positive. The major cellular fatty acids of the novel strain were summed feature 4 (comprising iso-C17 : 1I and/or anteiso-C17 : 1B, 36.8 %), iso-C15 : 0 (22.3 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 6.2 %). The DNA G+C content of strain GCM0142T was 48.9 mol% and the major quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, two unknown aminolipids (AL1-2), an unknown aminophospholipid, five unknown lipids (L1-5) and an unknown glycolipid. On the basis of the
Strain JC267T was isolated from pebbles collected from Pingleshwar beach, Gujarat, India. Cells are Gram-stain-positive, facultatively anaerobic, non-motile rods forming sub-terminal endospores in swollen ellipsoidal to oval sporangia. Strain JC267T contains anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0 as major (|5 %) cellular fatty acids. Polar lipids include phosphatidylglycerol, phospholipids (PL1-3), glycolipids (GL1-2) and an unidentified lipid. Cell-wall amino acids are composed of diagnostic meso-diaminopimelic acid, dl-alanine and a small amount of d-glutamic acid. The genomic DNA G+C content of strain JC267T is 45.5 mol%. The 16S rRNA gene sequence of strain JC267T showed highest sequence similarities of | 98.41 % with all species of the genus Bacillus when subjected to EzTaxon-e blast analysis. The reassociation values based on DNA-DNA hybridization of strain JC267T with Bacillus halosaccharovorans IBRC-M 10095T and Bacillus niabensis JCM 16399T were 26
TY - JOUR. T1 - Preliminary aqnalysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. AU - Chow, S.. AU - Ueno, Y.. AU - Toyokawa, M.. AU - Oohara, I.. AU - Takeyama, Haruko. PY - 2009/6. Y1 - 2009/6. N2 - Length and guanine-cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 ...
Redundancy of the genetic code implies that there are more codons than amino acids. Consequently, many amino acids are encoded by more than one codon, which are known as synonymous codons. As a result, some substitutions between these codons are silent and do not change the coded amino acid. For example, in the case of the codons known as fourfold degenerated (4FD), the third codon positions can be freely changed to any nucleotide, without consequences for the coded amino acid, and subsequently for protein composition and function. However, synonymous codons are not used uniformly in real protein coding sequences (e.g., Comeron 2004; Grantham et al. 1980; Ikemura 1985; Plotkin and Kudla 2011; Sharp and Li 1986). Such preference of one synonymous codon over others is commonly known as codon usage bias (Sharp and Li 1986). Usage can differ for various genomes and genes within one genome, and even within a single gene.. As far as the evolution of codon bias is concerned, two explanations, which are ...
Argos, P., Rossmann, M.G., Grau, U.M., Zuber, A., Frank, G. and Tratschin, J.D. (1979). «Thermal stability and protein structure». Biochemistry 18: pp. 5698-5703. • Dobzhansky, T. (1951). Genetics and the Origin of Species, 2ª ed.. Columbia University Press, New-York • Galtier, N. and Lobry, J.R. (1997). «Relationships between genomic G+C content, RNA secondary structure, and optimal growth temperature in prokaryotes». Journal of Molecular Evolution 44: pp. 632-636. • Gu, X., Hewett-Emmett, D. and Li, W-H. (1998). «Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria». Genetica 102/103: pp. 383-391. [1] • Graur, D. y [Wen-Hsiung Li (2000). Fundamentals of Molecular Evolution (second edition). Sinauer Associates. ISBN 0-87893-266-6. • Muto, A. and Osawa, S. (1987). «The guanine and cytosine content of genomic DNA and bacterial evolution». Proceedings of the National Academy of Sciences 84: pp. 166-169. [2] • Nei, M. ...
(2017) B. Miller et al. Biomedical Genetics and Genomics. It is well-documented that codon usage biases affect gene translational efficiency; however, it is less known if viruses share their hosts codon usage motifs. We determined that human-infecting viruses share similar codon usage biases as ...
GENEWIZ is widely known for reliability and completion of projects with a wide range of complexity levels including repetitive and sequences with high or low GC content. Our 99.9% delivery rate makes us the partner of choice for top research institutions across the world. Our many years of synthetic gene assembly experience provide endless opportunities to create any custom synthetic DNA sequence for your synthetic biology research ...
What is DNA? A DNA sequence contains only the letters A, C, G and T. (Each letter represents a small molecule, and a DNA sequence is a ``macromolecular chain of them.) Each letter in a DNA sequence is called a base, basepair, or nucleotide. Normally, DNA occurs as a double strand where each A is paired with a T and vice versa, and each C is paired with a G and vice versa. The reverse complement of a DNA sequence is formed by reversing the letters, interchanging A and T and interchanging C and G. Thus the reverse complement of ACCTGAG is CTCAGGT. What is a genome? A genome is all of an organisms DNA sequence. Each nucleus in one of your cells contains its own copy of your genome, which is about 3 billion letters. (More accurately, each cell has two nearly identical copies of the genome, except that the X and Y chromosomes are even more complicated.) Replication is the process of duplicating the genome when a cell divides. DNA composition. The genome of a warm-blooded animal is divided into ...
A new high-alkaline protease (ALTP) was purified to homogeneity from a culture of the strictly anaerobic and extremely alkaliphilic Alkaliphilus transvaale
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In bacteria, one example of such a characteristic is called the "G+C content." Recall that DNA is made up of nucleotides: A, T, G and C. The A and T pair together (A+T) in the DNA double helix, as do the G and C (G+C). After a bacterias genome is sequenced, the G+C content is calculated simply by adding up all the Gs and Cs and dividing that number by the total number of nucleotides. The percentage, which can range from 13% to 75%, tends to be characteristic of the bacterial species. Why one species is, say, 47% and another is 58% is thought to be due solely to chance. Luck of the draw ...
The National Aquarium is excited to announce the addition of Living Seashore, an interactive exhibit opening in spring 2015 where guests can explore the shore and touch the animals that live between the tides.
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Parablechnum roraimense and P. paucipinna spp. nov. (Blechnaceae: Polypodiopsida), lectotypification of P. stuebelii , and citation corrections in the family
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다음은 2011년 렐리아르트(Leliaert) 등이 제안하고,[4] 2016년 실라(Silar)가 수정했으며[5] 2016년 렐리아르트[6]와 2017년 로페스 도스 산토스(Lopes dos Santos) 등의 녹조식물 분류군 연구,[7] 2015년 노비코프(Novíkov)와 바라바스-크라스니(Barabaš-Krasni) 연구,[8] 산체스-바라칼도(Sánchez-Baracaldo) 연구에 기초한 녹조식물 계통 분류이다.[9][10][11] ...
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A Gram-staining-positive, cocci, halotolerant bacterial strain, designated as SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurs at temperatures in the range between 25-37 °C (optimum 30 °C), pH 7.0-11.0 (optimum 8.0) and at NaCl concentrations up to 25 .0 % (optimum 15.0 %). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6 %) followed by Salinicoccus halodurans W24T (96.6 %). The predominant polar lipids are diphosphatidylglycerol (DPG), phosphatidylinositol (PI) and phosphatidylglycerol (PG). The major cellular fatty acids are iso-C15: 0, anteiso-C15: 0, iso-C17: 0 and anteiso C17: 0. The draft genome of strain SV-16T consisted of 2,591,284 bp with G+C content of 48.7 mol %. On the basis of the phenotypic characteristics and genotypic ...
An obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3ENT, was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3–2.4 µm long by 0.30–0.75 µm wide) with single flagella. The strain grew at 10–37 °C (optimum 25–30 °C) and at pH 4.5–9.5 (optimum 5.0–7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3ENT was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3ENT was identified as Asticcacaulis biprosthecium DSM 4723T (97.2 % 16S rRNA gene sequence similarity) and the DNA–DNA hybridization value between strain CGM1-3ENT and A. biprosthecium DSM 4723T was less than 24.5 %. Strain ...
A bacterial strain, B5-2(T), was isolated from an ice core drilled from Muztagh Glacier, China. Strain B5-2(T) was a Gram-stainnegative, short rod-shaped, motile by polar flagella, aerobic bacterium. The major fatty acids of strain B5-2(T) were summed feature 8 (C-18 : 1 omega 7c and/ or C-18 : 1 omega 6c) and iso-C-13 : 0. The G+C content of the DNA from strain B5-2(T) was 69.3 mol%. The predominant isoprenoid quinone of strain B5-2(T) was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified phospholipid and sulfoquinovosyldiacylglycerol. Comparative 16S rRNA gene sequence analysis revealed that the novel strain B5-2(T) shared highest similarity (96.7 %) with Aureimonas altamirensis S21B(T). On the basis of the results of this polyphasic study, strain B5-2(T) represents a novel species of the genus Aureimonas, for which the name Aureimonas glaciei sp. nov. is ...
The type species for the genus Skermanella is Skermanella parooens ACM 2042T, which was originally proposed as Conglomeromonas largomobilis subsp. parooensis by Skerman et al. in 1983 [1]. Later, it was transferred to the genus Skermanella (family Rhodospirillaceae) on the basis of phylogenetic evidence and phenotypic characteristics, especially the inability to fix nitrogen [2,3]. At present, this genus comprises four validly published species, Skermanella parooensis [3], Skermanella aerolata [4], Skermanella xinjiangensis [5] and Skermanella stibiiresistens [6], which were isolated from fresh water, air, sandy soil and a coal mine, respectively.. Skermanella was characterized as a Gram-negative, non-spore-forming bacterium with unicellular and multicellular phases of growth, an obligate chemo-organotroph and facultative anaerobe, unable to fix nitrogen, and with a high DNA G+C content. To the best of our knowledge, genome information for Skermanella members is still not available. In this ...
A bacterium previously isolated from a diseased colony of the scleractinian coral Dichocoenia stokesi (common name elliptical star coral) was subjected to a detailed polyphasic taxonomic characterization. The isolate, designated WP1T, was halophilic and strictly aerobic and formed golden-orange-pigmented colonies after prolonged incubation. Cells of WP1T were Gram-negative, rod-shaped and showed a characteristic branching rod morphology. Chemotaxonomically, WP1T was characterized by having Q-10 as the major respiratory lipoquinone and sym-homospermidine as the main component of the cellular polyamine content. The predominant constituent in the cellular fatty acid profile was C18 : 1 ω7c, along with C19 : 0 cyclo ω8c and C16 : 0. Other fatty acids present in smaller amounts were C17 : 0, C18 : 0, C16 : 1 ω7c, C20 : 1 ω7c and C18 : 1 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Minor amounts of diphosphatidylglycerol,
A novel Gram-positive, aerobic, actinobacterial strain, CF6/1T, was isolated in 2007 during environmental screening of arid desert soil in the Sahara near to Ourba, Chad. The isolate was found to grow best in a temperature range of 20-37 °C and at pH 6.0-8.5 and showed no NaCl tolerance, forming black-coloured and nearly circular colonies on GYM agar. Chemotaxonomic and molecular characteristics determined for the isolate match those previously described for members of the genus Geodermatophilus. The DNA G + C content of the novel strain was determined to be 74.9 mol %. The peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The main phospholipids were determined to be phosphatidylethanolamine, phosphatidylinositol, phosphatidylcholine, diphosphatidylglycerol and traces of phosphatidylglycerol; MK-9(H4) was identified as the dominant menaquinone and galactose as the diagnostic sugar. The major cellular fatty acids were found to be the branched-chain ...
Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons). There are 64 different codons (61 codons encoding for amino acids plus 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others-that is, a greater frequency of one will be found than expected by chance. How such biases arise is a much debated area of molecular evolution. Codon usage tables detailing genomic codon usage bias for most organisms in GenBank and RefSeq can be found in the HIVE-Codon Usage ...
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model ...
16. A method of stabilizing a spine with a spinal stabilization device comprising a rod-shaped implant comprising a continuous one-piece rod-shaped member having a first end and a second end opposite the first end along a longitudinal axis, the rod-shaped member being made from a plastic material exhibiting flexibility, a longitudinal bore provided in the rod-shaped member, a reinforcing rod accommodated in the bore and made from a more rigid material than the material of the rod-shaped member, the reinforcing rod having a first end and a second end, wherein the reinforcing rod is slidable in the bore; and wherein the reinforcing rod comprises a stop contacting the rod-shaped member to limit movement of the reinforcing rod relative to the rod-shaped member, and at least two bone anchoring elements, each bone anchoring element having a receiving part for receiving the rod-shaped member, the method comprising:attaching the first bone anchoring element to a bone or vertebra;attaching the second ...
Expression breadth and synonymous substitution patterns are most probably due to gene length effects: The above results are suggestive of selection possibly playing a role in codon usage bias in humans. However, as stated earlier, genes of different length are likely to have different MCB values owing to the nature of the method. Indeed, if we randomize our sequences and measure the mean MCB for 1000 simulants for each of our genes, we find that the MCB, on average, is higher for shorter genes. This is to be expected of any statistic that employs a multinomial distribution and applies equally to the method of Karlin and Mrazek.. Importantly, it so happens that in our data set longer genes have a slightly higher rate of synonymous substitutions and are not expressed in as broad a range of tissues. Therefore, plotting mean MCB for the randomized genes against breadth of expression for the real gene, we still find a weak positive correlation of the order of magnitude reported for the real genes (P ...
General Information: The species type strain, originally isolated from a human gas gangrene patient. Causative agent of gas gangrene. This genus comprises about 150 metabolically diverse species of anaerobes that are ubiquitous in virtually all anoxic habitats where organic compounds are present, including soils, aquatic sediments and the intestinal tracts of animals and humans. This shape is attributed to the presence of endospores that develop under conditions unfavorable for vegetative growth and distend single cells terminally or sub-terminally. Spores germinate under conditions favorable for vegetative growth, such as anaerobiosis and presence of organic substrates. It is believed that present day Mollicutes (Eubacteria) have evolved regressively (i.e., by genome reduction) from gram-positive clostridia-like ancestors with a low GC content in DNA. Known opportunistic toxin-producing pathogens in animals and humans. Some species are capable of producing organic solvents (acetone, ethanol, ...
1. A comparison is made of several procedures for the extraction of tocopherols and isoprenoid quinones from plant tissues. 2. Gradient-elution column chromatography on acid-washed alumina efficiently separates the isoprenoid quinones and tocopherols into groups that can then be assayed spectrophotometrically or, with the tocopherols, separated into their individual components and determined by gas-liquid chromatography. 3. This improved analytical procedure was used to study the distribution of the tocopherols and of ubiquinone in the ungerminated wheat grain.. ...
4Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Italy. The AUG start codon context features have been investigated by analyzing eukaryotic mRNAs belonging to various taxonomic groups. The functional relevance of each specific position surrounding the AUG start codon has been established as a function of the measured shift between base composition observed at that particular position, and base composition averaged over all the 5 untranslated regions. A more detailed analysis carried out on human genes belonging to different isochores showed significant isochore-specific features that cannot be explained only by a mutational bias effect.. The most represented heptamers spanning from position -3 to +4 with respect to the initiator AUG have been determined for mRNAs belonging to different taxonomic groups and a web page utility has been set up (http://bigarea.area.ba.cnr.it:8000/BioWWW/ATG.html) to determine the relative abundance of a user submitted oligonucleotide context ...
PUZZLE VERSION 2.4 NOW AVAILABLE!! ==================================== Some *very* useful new features have been added to the PUZZLE program, partially due to requests of users of earlier versions: * AUTOMATIC RECOGNITION OF THE DATA TYPE. Depending on the input file PUZZLE switches automatically to the nucleotide or amino acid mode. * AUTOMATIC SELECTION OF THE MODEL OF SEQUENCE EVOLUTION. If the data set contains amino acids PUZZLE recogizes whether the amino acids are encoded on mtDNA or on nuclear DNA and selects accordingly one of the corresponding models of sequence evolution (Dayhoff, JTT, mtREV). If the data set consists of nucleotides the transition/transversion parameter is estimated by a maximum likelihood prodedure from the data. Thus, the Ts/Tv parameter needs not to be specified! * CHI^2 TEST ON BASE COMPOSITION. PUZZLE checks with the help of a 5% level chi^2 test whether the base composition of each taxon is identical with the average that serves as a basis for the maximum ...
Nov 01 11:58:15 * Lensman ([email protected]) has joined #knownspace Nov 01 12:52:54 * AgincourtDB ([email protected]) has joined #knownspace Nov 01 12:53:20 ,AgincourtDB, boo Nov 01 12:58:02 * AgincourtDB is now known as Agin-afk Nov 01 12:59:01 ,Lensman, Hi Aggie! Nov 01 13:01:55 ,Agin-afk, hey Nov 01 13:02:03 ,Agin-afk, went downstairs to get some coffee Nov 01 13:02:10 * Agin-afk is now known as AgincourtDB Nov 01 13:03:30 ,Lensman, I dont have you on my Niven chat "scorecard". Where do you live Aggie? (And is that the right nickname?) Nov 01 13:03:37 ,AgincourtDB, yup Nov 01 13:03:40 ,AgincourtDB, Gaithersburg MD Nov 01 13:03:55 ,Lensman, East coast, okay. Nov 01 13:04:12 ,Lensman, You said "coffee", I thought maybe it was morning where you live. Nov 01 13:04:22 ,AgincourtDB, no I just need coffee all day long hehe Nov 01 13:04:43 ,Lensman, I forgot to send out the Niven chat reminder yesterday, we may have some people who forgot about the chat today. Nov 01 13:05:03 ...
User:Neil R Gottel,Neil R Gottel]] 16:45, 28 February 2013 (EST): Different organisms will differ in the amount of each tRNA that corresponds to each codon. Certain codons are rare in some species, while common in others. So, if youre putting a jellyfish gene into E. coli, then the codon usage is likely not optimized. Then production of that genes product will be slower/lower (because it takes longer to produce a peptide if the ribosome is waiting around for a rare tRNA to come by). However, according to this OWW page on [[Codon usage optimization]], and specifically [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007002 this paper], the most important factor to consider is which tRNAs are charged (that is, get amino acids attached to them) when the cell is starving, and to favor using the corresponding codons when optimizing your gene. I havent actually done this sort of optimization though, so hopefully someone else more experienced can chime in ...
Sea salt is the natural form of salt and is said to be a lot healthier than iodized salt. Many people favor the use of iodized salt over sea salt due to their lack of understanding of its benefits. If you look around in the grocery store, you will find all sorts of foods already seasoned with iodized salt. It is best to either cook your own food with sea salt or find special products made with natural sea salt.
New and Refurbished Dental Equipment at Affordable Prices 6 Pin Swivel Connector (ISO-C) Multiflex™ [VKS6] - 6 Pin Swivel Connector ISO-C 6 pin swivel with bulb.
... Hotel Palace L zn novy smokovec. L zn Nov Smokovec ubytov n v hotelu Palace Vysok Tatry. k pele nov smokovec. L zn nov smokovec Hotel Palace. L zn Smokovec Smokovce.
An illustrative embodiment of a computer-implemented method to identify expertise using interaction metrics receives a user identity to form an identified user, receives usage information associated with the identified user to form received information and identifies usage patterns in the received information to form identified usage patterns. The computer-implemented method further applies assessment factors to the identified usage patterns and received information, calculates a ranking for the identified user to form a calculated ranking and assigns the calculated ranking to the identified user.
On-line rezervace zájezdu Nové Lázně - Relaxing Spa Holiday do hotelu Nové Lázně. Ubytování v Nové Lázně je zárukou kvaitní dovolené v Česká republika - Czech Republic - Marianske Lazne. vlastní doprava.
Genetic information is written by a variation in sequence on the one hand, and the physical stability of the double-stranded structure is determined by the base composition on the other hand. … DNA...
Thermobaculum terrenum ATCC ® BAA-798D-5™ Designation: Genomic DNA from Thermobaculum terrenum strain YNP1 (ATCC ® BAA-798™) TypeStrain=False Application:
channel name="displays" version="1.0", ,property name="Default" type="empty", ,property name="VGA-1" type="string" value="Idek Iiyama 23", ,property name="Active" type="bool" value="true"/, ,property name="Resolution" type="string" value="1920x1080"/, ,property name="RefreshRate" type="double" value="60.000000"/, ,property name="Rotation" type="int" value="90"/, ,property name="Reflection" type="string" value="0"/, ,property name="Primary" type="bool" value="false"/, ,property name="Position" type="empty", ,property name="X" type="int" value="0"/, ,property name="Y" type="int" value="0"/, ,/property, ,/property, ,property name="DVI-0" type="string" value="Digital display", ,property name="Active" type="bool" value="true"/, ,property name="Resolution" type="string" value="1920x1080"/, ,property name="RefreshRate" type="double" value="60.000000"/, ,property name="Rotation" type="int" value="90"/, ,property name="Reflection" type="string" value="0"/, ,property name="Primary" type="bool" ...
3Oblastn nemocnice Mlad Boleslav P nov z klad Espumil roz i uje mo nosti individu ln p pravy l iv v l k rn ch. l nek uv d vyu it pro l iv l tky b n pou van v dermatologii, jako jsou dexamethason, ichthamol, mikonazol, chlorh...
Vážení zákazníci,. vo štvrtok 17.2.2011 prechádzame na nový informačný systém. Prosime klientov o strpenie pri vybavovaní na recepcii.. Ďakujeme za porozumenie.. ...
is supplied, session_name() modifies the HTTP cookie (and output content when session.transid is enabled). Once the HTTP cookie is sent, session_name() raises error. session_name() must be called before session_start() for the session to work properly. The session name is reset to the default value stored in session.name at request startup time. Thus, you need to call session_name() for every request (and before session_start() is called). ...
I have named all of our other 4 children and my husband is naming our last baby. He wants to name her after himself in a sense but still give me my...
TCDRVDCK (*) OWC Drive Dock with USB-C (USB 3.1 Gen 2) Dual Drive Bay Solution. Add up to two 2.5" and 3.5" SATA drives. Connect via USB 3.1 Gen 2 (up to 10Gb/s). Internal power with independent power switches. *New, Open Box*
The CORSAIR Force MP600 Gen4 PCIe x4 NVMe M.2 SSD provides extreme storage performance, using Gen4 PCIe technology to achieve blazing fast sequential read speeds of up to 4,950MB/s.
When you see such an error message, check whether the script incorrectly changed a method name. If you find the method name in the second column of the table below, look in the first column to see the methods original name. You can then edit the program by hand, changing the error-causing line to use the original name. For example, to correct the error above, you should change ...
I think its about 80,000 names so we go to number 10 with a list of names so we can start the ball rolling in the political world so please more names !!!!!!!!!!!!!.Thanks mark
I am having a hard time coming up with a cool yet not cliche Adbenture Group Name. You know the name you call your D&D party group...its official company name. Any ideas?
d66 Disease Names - Ever needed a name right now and all you could think of was Bob? Do you want quick descriptions and details
d66 Disease Names - Ever needed a name right now and all you could think of was Bob? Do you want quick descriptions and details
Is there a special name for the stress mark itself (sometimes in the phonetic explanation there are forward-slashes and back-slashes)? Do they have names? I thought the rule was: one word, one stress? Please Help.
Like people, not all animals are the same. Some have gone on to make a name for themselves in this world, and considering the name of this list you can
에리스리톨을 설탕 대체 감미료 소재로 사용하기 위한 기초 자료를 얻기 위하여 치석의 원인균인 S. mutans KCTC 3065와 치아 부식의 원인균인 L. acidophillus를 이용하여 난충치성 시험을 하였고 기타 생리 특성으로 젖산균을 이용한 발효성 시험 그리고 마우스를 이용한 소장 내성력 시험을 주로 설탕, 크실리톨, 소르비...
மரபு நூலிழையில் உள்ள குறிப்பிட்ட ஒரு பகுதியைப் பெருக்குவதற்கு இந்தத் தொழில்நுட்பம் உதவுகின்றது. இலக்குப் பகுதியானது பொதுவாக 0.1-10 கிலோ தாங்கிச் சோடிகளைக் (kilo base pairs - kb) கொண்டதாக இருக்கும். ஆனாலும் ஒரு சில தாக்கங்கள் 40 கிலோ தாங்கிச் சோடிகள் வரை பெருக்கும் தன்மை கொண்டன.[2] குறிப்பிட்ட பகுதியின் பெருக்கமானது வழங்கப்படும் பொருட்களின் அளவில் தங்கியிருக்கும். செயற்பாட்டிற்குத் ...
Zbavte sa suchých a popraskaných pier. S kolagénovou maskou Pilaten budú Vaše pery jemnejšie ako kedykoľvek predtým! Plné pery priťahujú pozornosť
Find and save ideas about Swag quotes on Pinterest. | See more ideas about Swag quotes tumblr, Nicki minaj real name and Nikki minaj before.
We have come up with two facts. One. the band name will include the word Rust. Two, Im still wondering about two. What do you like better. I dont...
The third letter (surely "v") is partly legible; the first two are not. The number of irrecoverable letters must be limited by the chicane which precedes the name.. ...
A Gram-stain-positive, aerobic, non-spore-forming, atrichous and short rod-shaped endophytic actinomycete, designated strain BGMRC 2075 , was isolated from the leaves of Kandelia candel, and was subjected to polyphasic characterization to unravel its taxonomic position. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BGMRC 2075 belongs to the genus Nocardioides ,showing the highest 16S rRNA gene sequence similarity to Nocardioides aestuarii JC2056 (96.1 %), Nocardioides agariphilus MSL-28 (95.1 %) andNocardioides islandiensis MSL-26 (95.1 %). The predominant cellular fatty acids of strain BGMRC 2075 were iso-C16 : 0, C17 : 1ω8c and C17 : 0. The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were composed of ribose and glucose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, ...
A novel halophilic actinomycete, strain H32T,was isolated froma Saharan soil sample collected in El-Oued province, south Algeria. The isolate was characterized by means of polyphasic taxonomy. Optimal growth was determined to occur at 28-32°C, pH 6.0-7.0 and in the presence of 15-25 %(w/v) NaCl. The strain was observed to produce abundant aerial mycelium, which formed long chains of rod-shaped spores at maturity, and fragmented substrate mycelium. The cell wall was determined to contain meso-diaminopimelic acid and the characteristic whole-cell sugars were arabinose and galactose. The predominant menaquinoneswere found to beMK-10(H4) andMK-9(H4). The predominant cellular fatty acids were determined to be anteiso C17:0, iso-C15:0 and iso-C16:0. The diagnostic phospholipid detected was phosphatidylcholine. Phylogenetic analyses based on the 16S rRNA gene sequence showed that this strain formed a distinct phyletic line within the radiation of the genus Actinopolyspora. The 16S rRNAgene sequence ...
The base composition of DNA was determined for individual chromosomes from the dipteran Chironomus tentans and for each one of six different segments of one of the chromosomes. The isolations were carried out by micromanipulation and the DNA purines were first extracted from the isolated components and afterwards separated by means of microelectrophoresis on a cellulose fiber. It was found that DNA from this material has an unusual composition corresponding to a guanine + cytosine content of about 30%. This composition was not a function of the polytenic condition but was also found for DNA from testis tissue. Furthermore Drosophila has a more traditional base composition for the bulk of DNA. Statistically significant variations in base data were found between whole chromosomes as well as between the segments from one of the chromosomes.. ...
Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usage in Brachypodium. We found that low- and high-GC content genes with different codon usage occur frequently in the genome.
Widdel 1981) Kuever 2006 may be the type and only species of the genus and the order GEBAproject. class represents a separate lineage within the which is only distantly related to most other members of this class. The closest relatives based on 16S rRNA gene sequence similarity values are the type strains of (87.6% sequence identity) and (87.2%) both belonging to the family within the order [9]. The most similar cloned 16S rRNA gene EUB-42 [10] shared only 95.5% sequence similarity with and was retrieved from anaerobic sludge. Strain 2st14T WYE-354 represents the only stress of this varieties obtainable from a tradition collection so far. Available data from cultivation 3rd party studies (environmental testing and genomic studies) didnt surpass 86% series similarity indicating that people of this varieties are limited to specific habitats which are undersampled generally in most conditions or are in low great quantity (status Oct 2010). The solitary genomic 16S rRNA series of stress 2st14T was ...
In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases on a DNA molecule that are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine).[1] This may refer to a specific fragment of DNA or RNA, or that of the whole genome. When it refers to a fragment of the genetic material, it may denote the GC-content of part of a gene (domain), single gene, group of genes (or gene clusters), or even a non-coding region. G (guanine) and C (cytosine) undergo a specific hydrogen bonding, whereas A (adenine) bonds specifically with T (thymine). The GC pair is bound by three hydrogen bonds, while AT pairs are bound by two hydrogen bonds. DNA with high GC-content is more stable than DNA with low GC-content; however, the hydrogen bonds do not stabilize the DNA significantly, and stabilization is due mainly to stacking interactions.[2] In spite of the higher thermostability conferred to the genetic ...
An obligately anaerobic bacterial strain designated T-1-35(T) was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35(T) stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8-1.0 3.5-15.0 m, and motile by means of two to four polar flagella. Cells of strain T-1-35(T) exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 C for 10 min. The temperature range for growth was 15-40 C, with an optimum at 35 C. The pH range for growth was 5.5-9.0, with an optimum at pH 8.0-8.5 (slightly alkaliphilic). Strain T-1-35(T) fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed ...
An industrial approach to protein production demands maximization of cloned gene expression, balanced with the recombinant hosts viability. Expression of toxic genes from thermophiles poses particular difficulties due to high GC content, mRNA secondary structures, rare codon usage and impairing the hosts coding plasmid replication. TaqII belongs to a family of bifunctional enzymes, which are a fusion of the restriction endonuclease (REase) and methyltransferase (MTase) activities in a single polypeptide. The family contains thermostable REases with distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI and a few enzymes found in mesophiles. While not being isoschizomers, the enzymes exhibit amino acid (aa) sequence homologies, having molecular sizes of ~120 kDa share common modular architecture, resemble Type-I enzymes, cleave DNA 11/9 nt from the recognition sites, their activity is affected by S-adenosylmethionine (SAM). We describe the taqIIRM gene design, cloning and expression
The genus Lysobacter belongs to the family Xanthomonadaceae within the Gammaproteobacteria and includes 13 named species: Lysobacter enzymogenes, L. antibioticus, L. gummosus, L. brunescens, L. defluvii, L. niabensis, L. niastensis, L. daejeonensis, L. yangpyeongensis, L. koreensis, L. concretionis, L. spongiicola, and L. capsici. Lysobacter spp. were originally grouped with myxobacteria because they shared the distinctive trait of gliding motility, but they uniquely display a number of traits that distinguish them from other taxonomically and ecologically related microbes including high genomic G+C content (typically ranging between 65 and 72%) and the lack of flagella. The feature of gliding motility alone has piqued the interest of many, since the role of gliding bacteria in soil ecology is poorly understood. In addition, while a number of different mechanisms have been proposed for gliding motility among a wide range of bacterial species, the genetic mechanism in Lysobacter remains unknown. ...
There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, the biased codon usage can be also a by-product of a general selection at the amino acid level interacting with nucleotide replacements. To evaluate the validity and strength of such effect, we superimposed more than 3.5 billion unrestricted mutational processes on the selection of non-synonymous substitutions based on the differences in physicochemical properties of the coded amino acids. Using a modified evolutionary optimization algorithm, we determined the conditions in which the effect on the relative codon usage is maximized. We found that the effect is enhanced by mutational processes generating more adenine and thymine than guanine and cytosine as well as more purines than pyrimidines. Interestingly, this effect is observed only under an unrestricted model of nucleotide ...
Bacteroides is a genus of Gram-negative, rod-shaped bacteria. Bacteroides species are non-endospore-forming, anaerobes, and may either be motile or non-motile, depending on the species.[1] The DNA base composition is 40-48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer. Bacteroides are normally commensal, making up the most substantial portion of the mammalian gastrointestinal flora,[2] where they play a fundamental role in processing of complex molecules to simpler ones in the host intestine. As many as 1010-1011 cells per gram of human feces have been reported.[3] They can use simple sugars when available, but the main source of energy is polysaccharides from plant sources. ...
king interactions (hydrogen bonding merely provides specificity of the pairing, not stability). As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands. In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart. In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single common shape, but some ...
We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution. We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.